tobiasko
commented
3 months ago FYI I figured out how to use alphapepDeep for library prediction, but I get the same error:
alphadia --output out --file 20240530_001_S569409_HeLaProteinDigest_5ug.d --fasta fgcz_9606_1spg_20230330.fasta --config prediction_timstof.yaml
Removed 0 of 1 files.
0:00:00.000294 PROGRESS: Searching 1 files:
0:00:00.000373 PROGRESS: 20240530_001_S569409_HeLaProteinDigest_5ug.d
0:00:00.000413 PROGRESS: Using library: None.
0:00:00.000445 PROGRESS: Using 1 fasta files:
0:00:00.000474 PROGRESS: fgcz_9606_1spg_20230330.fasta
0:00:00.000509 PROGRESS: Saving output to out.
0:00:00.000254 PROGRESS: _ _ ___ ___ _
0:00:00.000361 PROGRESS: __ _| |_ __| |_ __ _| \_ _| /_\
0:00:00.000400 PROGRESS: / _` | | '_ \ ' \/ _` | |) | | / _ \
0:00:00.000430 PROGRESS: \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.000458 PROGRESS: |_|
0:00:00.000486 PROGRESS:
0:00:00.000517 PROGRESS: version: 1.6.1
0:00:00.000551 PROGRESS: hostname: fgcz-c-073
0:00:00.000605 PROGRESS: date: 2024-06-05 14:05:43
0:00:00.000637 PROGRESS: =================== Environment ===================
0:00:00.000670 PROGRESS: alphatims : 1.0.8
0:00:00.000700 PROGRESS: alpharaw : 0.4.5
0:00:00.000729 PROGRESS: alphabase : 1.2.3
0:00:00.000758 PROGRESS: alphapeptdeep : 1.1.9
0:00:00.000787 PROGRESS: directlfq : 0.2.19
0:00:00.000814 PROGRESS: ===================================================
0:00:00.000857 INFO: loading default config from /home/tobiasko/miniconda3/envs/alphadia/lib/python3.9/site-packages/alphadia/constants/default.yaml
0:00:00.017267 INFO: ├──version: 1
0:00:00.017323 INFO: ├──general
0:00:00.017365 INFO: │ ├──thread_count: 10
0:00:00.017400 INFO: │ ├──thread_count: 32 (user defined)
0:00:00.017437 INFO: │ ├──reuse_calibration: False
0:00:00.017475 INFO: │ ├──reuse_quant: False
0:00:00.017510 INFO: │ ├──astral_ms1: False
0:00:00.017545 INFO: │ ├──log_level: INFO
0:00:00.017581 INFO: │ ├──wsl: False
0:00:00.017616 INFO: │ ├──mmap_detector_events: False
0:00:00.017651 INFO: │ └──use_gpu: True
0:00:00.017685 INFO: ├──library_loading
0:00:00.017721 INFO: │ └──rt_heuristic: 180
0:00:00.017754 INFO: ├──library_prediction
0:00:00.017790 INFO: │ ├──predict: False
0:00:00.017822 INFO: │ ├──predict: True (user defined)
0:00:00.017856 INFO: │ ├──enzyme: trypsin
0:00:00.017891 INFO: │ ├──fixed_modifications: Carbamidomethyl@C
0:00:00.017927 INFO: │ ├──variable_modifications: Oxidation@M;Acetyl@Protein N-term
0:00:00.017963 INFO: │ ├──max_var_mod_num: 2
0:00:00.017998 INFO: │ ├──missed_cleavages: 1
0:00:00.018030 INFO: │ ├──precursor_len
0:00:00.018066 INFO: │ │ ├──7
0:00:00.018101 INFO: │ │ └──35
0:00:00.018135 INFO: │ ├──precursor_charge
0:00:00.018175 INFO: │ │ ├──2
0:00:00.018209 INFO: │ │ └──4
0:00:00.018242 INFO: │ │ └──3 (user defined)
0:00:00.018275 INFO: │ ├──precursor_mz
0:00:00.018311 INFO: │ │ ├──400
0:00:00.018346 INFO: │ │ └──1200
0:00:00.018379 INFO: │ ├──fragment_mz
0:00:00.018414 INFO: │ │ ├──200
0:00:00.018449 INFO: │ │ └──2000
0:00:00.018489 INFO: │ ├──nce: 25.0
0:00:00.018525 INFO: │ ├──fragment_types: b;y
0:00:00.018560 INFO: │ ├──max_fragment_charge: 2
0:00:00.018595 INFO: │ ├──instrument: Lumos
0:00:00.018627 INFO: │ ├──instrument: Timstof (user defined)
0:00:00.018662 INFO: │ └──checkpoint_folder_path: None
0:00:00.018696 INFO: ├──search
0:00:00.018732 INFO: │ ├──channel_filter: 0
0:00:00.018767 INFO: │ ├──exclude_shared_ions: True
0:00:00.018803 INFO: │ ├──compete_for_fragments: True
0:00:00.018837 INFO: │ ├──target_num_candidates: 2
0:00:00.018872 INFO: │ ├──target_ms1_tolerance: 15
0:00:00.018906 INFO: │ ├──target_ms2_tolerance: 15
0:00:00.018943 INFO: │ ├──target_mobility_tolerance: 0.04
0:00:00.018979 INFO: │ ├──target_rt_tolerance: 60
0:00:00.019013 INFO: │ ├──quant_window: 3
0:00:00.019049 INFO: │ └──quant_all: True
0:00:00.019083 INFO: ├──search_advanced
0:00:00.019118 INFO: │ └──top_k_fragments: 12
0:00:00.019152 INFO: ├──calibration
0:00:00.019187 INFO: │ ├──min_epochs: 3
0:00:00.019233 INFO: │ ├──max_epochs: 20
0:00:00.019269 INFO: │ ├──batch_size: 8000
0:00:00.019305 INFO: │ ├──recalibration_target: 200
0:00:00.019340 INFO: │ ├──final_full_calibration: False
0:00:00.019376 INFO: │ └──norm_rt_mode: linear
0:00:00.019409 INFO: ├──search_initial
0:00:00.019445 INFO: │ ├──initial_num_candidates: 1
0:00:00.019481 INFO: │ ├──initial_ms1_tolerance: 30
0:00:00.019516 INFO: │ ├──initial_ms2_tolerance: 30
0:00:00.019552 INFO: │ ├──initial_mobility_tolerance: 0.08
0:00:00.019587 INFO: │ └──initial_rt_tolerance: 240
0:00:00.019620 INFO: ├──selection_config
0:00:00.019657 INFO: │ ├──peak_len_rt: 10.0
0:00:00.019694 INFO: │ ├──sigma_scale_rt: 0.5
0:00:00.019730 INFO: │ ├──peak_len_mobility: 0.01
0:00:00.019766 INFO: │ ├──sigma_scale_mobility: 1.0
0:00:00.019801 INFO: │ ├──top_k_precursors: 3
0:00:00.019836 INFO: │ ├──kernel_size: 30
0:00:00.019871 INFO: │ ├──f_mobility: 1.0
0:00:00.019907 INFO: │ ├──f_rt: 0.99
0:00:00.019943 INFO: │ ├──center_fraction: 0.5
0:00:00.019979 INFO: │ ├──min_size_mobility: 8
0:00:00.020014 INFO: │ ├──min_size_rt: 3
0:00:00.020049 INFO: │ ├──max_size_mobility: 20
0:00:00.020084 INFO: │ ├──max_size_rt: 15
0:00:00.020119 INFO: │ ├──group_channels: False
0:00:00.020154 INFO: │ ├──use_weighted_score: True
0:00:00.020190 INFO: │ ├──join_close_candidates: False
0:00:00.020226 INFO: │ ├──join_close_candidates_scan_threshold: 0.6
0:00:00.020263 INFO: │ └──join_close_candidates_cycle_threshold: 0.6
0:00:00.020297 INFO: ├──scoring_config
0:00:00.020333 INFO: │ ├──score_grouped: False
0:00:00.020368 INFO: │ ├──top_k_isotopes: 3
0:00:00.020403 INFO: │ ├──reference_channel: -1
0:00:00.020437 INFO: │ ├──precursor_mz_tolerance: 10
0:00:00.020473 INFO: │ └──fragment_mz_tolerance: 15
0:00:00.020506 INFO: ├──multiplexing
0:00:00.020542 INFO: │ ├──enabled: False
0:00:00.020577 INFO: │ ├──target_channels: 4,8
0:00:00.020612 INFO: │ ├──decoy_channel: 12
0:00:00.020647 INFO: │ ├──reference_channel: 0
0:00:00.020682 INFO: │ └──competetive_scoring: True
0:00:00.020715 INFO: ├──fdr
0:00:00.020753 INFO: │ ├──fdr: 0.01
0:00:00.020788 INFO: │ ├──group_level: proteins
0:00:00.020823 INFO: │ ├──competetive_scoring: True
0:00:00.020857 INFO: │ ├──keep_decoys: False
0:00:00.020893 INFO: │ ├──channel_wise_fdr: False
0:00:00.020927 INFO: │ └──inference_strategy: heuristic
0:00:00.020960 INFO: ├──search_output
0:00:00.021009 INFO: │ ├──peptide_level_lfq: False
0:00:00.021047 INFO: │ ├──precursor_level_lfq: False
0:00:00.021082 INFO: │ ├──min_k_fragments: 12
0:00:00.021117 INFO: │ ├──min_correlation: 0.9
0:00:00.021152 INFO: │ ├──num_samples_quadratic: 50
0:00:00.021187 INFO: │ ├──min_nonnan: 3
0:00:00.021222 INFO: │ └──normalize_lfq: True
0:00:00.021256 INFO: ├──optimization_manager
0:00:00.021291 INFO: │ ├──fwhm_rt: 5
0:00:00.021327 INFO: │ ├──fwhm_mobility: 0.01
0:00:00.021362 INFO: │ └──score_cutoff: 0
0:00:00.021395 INFO: ├──transfer_learning
0:00:00.021431 INFO: │ ├──enabled: False
0:00:00.021466 INFO: │ ├──fragment_types: b;y
0:00:00.021500 INFO: │ ├──max_charge: 2
0:00:00.021534 INFO: │ ├──top_k_samples: 3
0:00:00.021570 INFO: │ ├──norm_delta_max: True
0:00:00.021605 INFO: │ ├──precursor_correlation_cutoff: 0.5
0:00:00.021641 INFO: │ └──fragment_correlation_ratio: 0.75
0:00:00.021675 INFO: └──calibration_manager
0:00:00.021709 INFO: ├──0
0:00:00.021745 INFO: │ ├──name: fragment
0:00:00.021785 INFO: │ └──estimators
0:00:00.021820 INFO: │ └──0
0:00:00.021857 INFO: │ ├──name: mz
0:00:00.021894 INFO: │ ├──model: LOESSRegression
0:00:00.021928 INFO: │ ├──model_args
0:00:00.021964 INFO: │ │ └──n_kernels: 2
0:00:00.021999 INFO: │ ├──input_columns
0:00:00.022035 INFO: │ │ └──mz_library
0:00:00.022070 INFO: │ ├──target_columns
0:00:00.022105 INFO: │ │ └──mz_observed
0:00:00.022140 INFO: │ ├──output_columns
0:00:00.022175 INFO: │ │ └──mz_calibrated
0:00:00.022211 INFO: │ └──transform_deviation: 1e6
0:00:00.022246 INFO: └──1
0:00:00.022282 INFO: ├──name: precursor
0:00:00.022316 INFO: └──estimators
0:00:00.022350 INFO: ├──0
0:00:00.022386 INFO: │ ├──name: mz
0:00:00.022421 INFO: │ ├──model: LOESSRegression
0:00:00.022455 INFO: │ ├──model_args
0:00:00.022491 INFO: │ │ └──n_kernels: 2
0:00:00.022525 INFO: │ ├──input_columns
0:00:00.022560 INFO: │ │ └──mz_library
0:00:00.022594 INFO: │ ├──target_columns
0:00:00.022629 INFO: │ │ └──mz_observed
0:00:00.022663 INFO: │ ├──output_columns
0:00:00.022698 INFO: │ │ └──mz_calibrated
0:00:00.022735 INFO: │ └──transform_deviation: 1e6
0:00:00.022768 INFO: ├──1
0:00:00.022804 INFO: │ ├──name: rt
0:00:00.022839 INFO: │ ├──model: LOESSRegression
0:00:00.022873 INFO: │ ├──model_args
0:00:00.022909 INFO: │ │ └──n_kernels: 6
0:00:00.022943 INFO: │ ├──input_columns
0:00:00.022978 INFO: │ │ └──rt_library
0:00:00.023012 INFO: │ ├──target_columns
0:00:00.023048 INFO: │ │ └──rt_observed
0:00:00.023082 INFO: │ └──output_columns
0:00:00.023117 INFO: │ └──rt_calibrated
0:00:00.023150 INFO: └──2
0:00:00.023186 INFO: ├──name: mobility
0:00:00.023222 INFO: ├──model: LOESSRegression
0:00:00.023256 INFO: ├──model_args
0:00:00.023292 INFO: │ └──n_kernels: 2
0:00:00.023326 INFO: ├──input_columns
0:00:00.023361 INFO: │ └──mobility_library
0:00:00.023396 INFO: ├──target_columns
0:00:00.023431 INFO: │ └──mobility_observed
0:00:00.023466 INFO: └──output_columns
0:00:00.023501 INFO: └──mobility_calibrated
0:00:00.023941 PROGRESS: No library provided. Building library from fasta files.
0:00:00.023982 INFO: Running FastaDigest
0:00:01.138726 INFO: Digesting fasta file
0:00:07.199373 INFO: Adding modifications
0:01:27.835186 INFO: Removing non-canonical amino acids
0:01:32.522871 INFO: Fasta library contains 2,906,923 precursors
0:01:32.523267 PROGRESS: Predicting library properties.
0:01:32.523360 INFO: Running PeptDeepPrediction
0:01:33.627932 INFO: Loading PeptDeep models from None
0:01:33.628085 INFO: Using external ms2 model: 'None/ms2.pth'
0:01:33.628149 INFO: -- This model file does not exist
0:01:33.628186 INFO: Using external rt model: 'None/rt.pth'
0:01:33.628219 INFO: -- This model file does not exist
0:01:33.628250 INFO: Using external ccs model: 'None/ccs.pth'
0:01:33.628281 INFO: -- This model file does not exist
0:01:33.628317 INFO: Predicting RT, MS2 and mobility
0:01:33.628398 INFO: Using multiprocessing with 32 processes ...
0:01:34.128267 INFO: Predicting rt,ms2,mobility ...
100%|██████████████████████████████████████████████████████████████████████████████| 46/46 [06:17<00:00, 8.21s/it]
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_yfjmf49s. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,372,928
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_l9ytepef. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,368,832
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_0872wxq5. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,368,832
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_01cm8g7i. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,372,928
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_zkz21dl5. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,377,024
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_oheiwmj4. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,377,024
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_hwkf05i3. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,372,928
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_ln8kefer. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,372,928
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_rtwztnzw. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,381,120
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_992f096a. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,393,408
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_rwotyy_y. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,393,408
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_g_c593ut. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,389,312
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_s2bb1gi6. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,393,408
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_miwyvhhp. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,397,504
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_hzepu2_w. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,401,600
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_hphp6wlh. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,405,696
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_kb673z2v. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,409,792
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_f3dwapd4. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,422,080
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap__ztuufhp. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,450,752
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_afeh13d4. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,442,560
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap__khooj_q. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,442,560
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_ut6gsm_t. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,446,656
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_rilq2p36. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,438,464
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_qquayx9h. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,442,560
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_es5a_gti. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,450,752
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_foy8ub29. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,450,752
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_97me0ud6. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,454,848
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_vknn593w. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,458,944
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_snhylqud. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,454,848
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_n3xuxiti. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,458,944
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap__9xwky1d. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,463,040
2024-06-05 14:13:36> WARNING: Temp mmap arrays were written to /tmp/temp_mmap_6pqhh3v7. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,487,616
0:07:55.477923 INFO: Adding fragment mz information
0:07:55.695896 INFO: Adding fragment intensity information
0:07:55.911700 INFO: Adding precursor information
0:07:56.374979 INFO: Running PrecursorInitializer
0:07:56.393164 INFO: Running AnnotateFasta
0:07:56.633350 INFO: Dropping decoys from input library before annotation
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████| 21097/21097 [00:03<00:00, 5569.13it/s]
0:08:16.039376 INFO: Running IsotopeGenerator
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 305/305 [00:26<00:00, 11.53it/s]
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_yd33bul5. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,372,928
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_jjdkhzbg. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,381,120
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_ha4om7er. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,381,120
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap__fivchnw. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,385,216
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_kiwwxbcn. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,385,216
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_28veo0k_. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,381,120
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_8pgdifgs. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,401,600
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_tbhllppn. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,397,504
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_0lycax56. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,397,504
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_mu18sp5r. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,401,600
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_8vnfl9vd. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,409,792
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_ii_ow3jz. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,417,984
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_tbkwf0z0. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,417,984
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_5n9ywlo2. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,417,984
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_pmh9s68u. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,417,984
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_z5lbc8w7. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,409,792
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_ynjaqc6z. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,413,888
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_lb0b8he0. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,430,272
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_x4fh0_pb. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,409,792
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_ms0hyixr. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,438,464
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_2wkmncva. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,442,560
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_bwtartvm. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,446,656
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_nmorjywk. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,446,656
0:08:46.434181 INFO: Running RTNormalization
0:08:46.434674 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:08:46.434753 INFO: Saving library to out/speclib.hdf
0:09:03.765550 INFO: Running DecoyGenerator
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_ont4_x64. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,360,640
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_u813xxth. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,360,640
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_uwq68k5d. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,364,736
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_fkjd_z0x. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,364,736
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_l_mpp3dc. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,364,736
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_di1jjl7w. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,364,736
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_kajf594t. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,368,832
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_xiptk87g. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,368,832
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_c_qgq5z5. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,368,832
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_q1pd51dz. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,360,640
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap__l0bcm8w. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,372,928
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_28teohjb. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,372,928
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap__3j67ke9. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,364,736
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_aepclcy7. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,397,504
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_ikyxz639. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,393,408
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_4o7lc2nf. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,413,888
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_lstn022l. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,422,080
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_7gxkkvk0. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,426,176
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_uyl47j4s. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,422,080
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_crmost2q. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,417,984
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap__pgilka3. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,417,984
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_7_6x3ruk. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,417,984
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_k4cqmk_p. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,426,176
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_0biipkb3. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,426,176
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_z8o42xl8. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,426,176
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_vcfzzqtn. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,438,464
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_rcwh_pyj. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,442,560
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_h4vhwvaj. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,446,656
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_m19sdg8k. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,467,136
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_bcpi84q6. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,467,136
WARNING:root:WARNING: Temp mmap arrays were written to /tmp/temp_mmap_9pb2y7x2. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,467,136
0:10:24.169449 INFO: Running FlattenLibrary
0:10:41.812157 INFO: Running InitFlatColumns
0:10:41.934608 INFO: Running LogFlatLibraryStats
0:10:41.934762 INFO: ============ Library Stats ============
0:10:41.934809 INFO: Number of precursors: 5,812,882
0:10:43.050704 INFO: thereof targets:2,906,923
0:10:43.050875 INFO: thereof decoys: 2,905,959
0:10:43.097010 INFO: Number of elution groups: 2,906,923
0:10:43.097164 INFO: average size: 2.00
0:10:43.304514 INFO: Number of proteins: 34,853
0:10:43.323776 INFO: Number of channels: 1 ([0])
0:10:43.324014 INFO: Isotopes Distribution for 4 isotopes
0:10:43.324056 INFO: =======================================
0:10:43.331964 PROGRESS: Starting Search Workflows
0:10:43.332274 PROGRESS: Loading raw file 1/1: 20240530_001_S569409_HeLaProteinDigest_5ug
0:10:43.333091 INFO: Importing data from 20240530_001_S569409_HeLaProteinDigest_5ug.d
0:10:43.333238 INFO: Using .d import for 20240530_001_S569409_HeLaProteinDigest_5ug.d
0:10:43.333328 INFO: Reading frame metadata for 20240530_001_S569409_HeLaProteinDigest_5ug.d
0:10:43.475878 INFO: Reading 16,032 frames with 147,808,814 detector events for 20240530_001_S569409_HeLaProteinDigest_5ug.d
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████| 16032/16032 [00:04<00:00, 3970.27it/s]
0:10:47.585830 INFO: Indexing 20240530_001_S569409_HeLaProteinDigest_5ug.d...
0:10:47.590809 INFO: Opening handle for 20240530_001_S569409_HeLaProteinDigest_5ug.d
0:10:47.594230 INFO: Fetching mobility values from 20240530_001_S569409_HeLaProteinDigest_5ug.d
0:10:47.594616 INFO: Closing handle for 20240530_001_S569409_HeLaProteinDigest_5ug.d
0:10:47.594981 INFO: Opening handle for 20240530_001_S569409_HeLaProteinDigest_5ug.d
0:10:47.597521 INFO: Fetching mz values from 20240530_001_S569409_HeLaProteinDigest_5ug.d
0:10:47.625688 INFO: Closing handle for 20240530_001_S569409_HeLaProteinDigest_5ug.d
0:10:47.625975 INFO: Indexing quadrupole dimension
0:10:47.722696 INFO: Transposing detector events
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:01<00:00, 15.78it/s]
0:10:50.474223 INFO: Finished transposing data
0:10:50.476380 INFO: Successfully imported data from 20240530_001_S569409_HeLaProteinDigest_5ug.d
0:10:51.225061 INFO: Initializing CalibrationManager
0:10:51.225536 INFO: Loading calibration config
0:10:51.225644 INFO: Calibration config: [{'name': 'fragment', 'estimators': [{'name': 'mz', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'transform_deviation': '1e6'}]}, {'name': 'precursor', 'estimators': [{'name': 'mz', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'transform_deviation': '1e6'}, {'name': 'rt', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated']}, {'name': 'mobility', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated']}]}]
0:10:51.225736 INFO: Calibration group :fragment, found 1 estimator(s)
0:10:51.225872 INFO: Calibration group :precursor, found 3 estimator(s)
0:10:51.225979 INFO: Initializing OptimizationManager
0:10:51.226095 INFO: initial parameter: fwhm_rt = 5
0:10:51.226171 INFO: initial parameter: fwhm_mobility = 0.01
0:10:51.226254 INFO: initial parameter: score_cutoff = 0
0:10:51.226386 PROGRESS: Initializing workflow 20240530_001_S569409_HeLaProteinDigest_5ug
0:10:51.226504 INFO: Initializing OptimizationManager
0:10:51.226543 INFO: initial parameter: current_epoch = 0
0:10:51.226573 INFO: initial parameter: current_step = 0
0:10:51.226602 INFO: initial parameter: ms1_error = 30
0:10:51.226630 INFO: initial parameter: ms2_error = 30
0:10:51.226658 INFO: initial parameter: rt_error = 240
0:10:51.226688 INFO: initial parameter: mobility_error = 0.08
0:10:51.226716 INFO: initial parameter: column_type = library
0:10:51.226744 INFO: initial parameter: num_candidates = 1
0:10:51.226772 INFO: initial parameter: recalibration_target = 200
0:10:51.226800 INFO: initial parameter: accumulated_precursors = 0
0:10:51.226828 INFO: initial parameter: accumulated_precursors_01FDR = 0
0:10:51.226856 INFO: initial parameter: accumulated_precursors_001FDR = 0
0:10:51.226900 INFO: Initializing FDRManager
0:10:51.226948 INFO: Loading classifier store from /home/tobiasko/miniconda3/envs/alphadia/lib/python3.9/site-packages/alphadia/constants/classifier
0:10:51.233268 PROGRESS: Applying channel filter using only: [0]
0:10:52.010025 PROGRESS: 2,035,650 target precursors potentially observable (871,273 removed)
0:10:53.104461 INFO: === checking if epoch conditions were reached ===
0:10:53.104845 INFO: ❌ ms1_error : 30.0000 > 15
0:10:53.104928 INFO: ❌ ms2_error : 30.0000 > 15
0:10:53.105020 INFO: ❌ rt_error : 240.0000 > 60
0:10:53.105096 INFO: ❌ mobility_error : 0.0800 > 0.04
0:10:53.105166 INFO: ❌ current_epoch : 0 < 3
0:10:53.105229 INFO: ==============================================
0:10:53.193871 INFO: calibration group: precursor, predicting mz
0:10:53.194194 WARNING: mz prediction was skipped as it has not been fitted yet
0:10:53.194243 INFO: calibration group: precursor, predicting rt
0:10:53.194311 WARNING: rt prediction was skipped as it has not been fitted yet
0:10:53.194347 INFO: calibration group: precursor, predicting mobility
0:10:53.194414 WARNING: mobility prediction was skipped as it has not been fitted yet
0:10:53.194470 INFO: calibration group: fragment, predicting mz
0:10:53.194539 WARNING: mz prediction was skipped as it has not been fitted yet
0:10:53.194593 PROGRESS: === Epoch 0, step 0, extracting elution groups 0 to 8000 ===
0:10:53.245348 PROGRESS: Extracting batch of 15568 precursors
0:10:56.731916 INFO: Duty cycle consists of 9 frames, 0.96 seconds cycle time
0:10:56.732125 INFO: Duty cycle consists of 945 scans, 0.00049 1/K_0 resolution
0:10:56.732177 INFO: FWHM in RT is 5.00 seconds, sigma is 1.11
0:10:56.732212 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 8.58
0:10:58.420786 INFO: Starting candidate selection
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████| 15568/15568 [00:39<00:00, 397.36it/s]
0:11:41.824747 ERROR: Search for 20240530_001_S569409_HeLaProteinDigest_5ug failed with error No objects to concatenate
Traceback (most recent call last):
File "/home/tobiasko/miniconda3/envs/alphadia/lib/python3.9/site-packages/alphadia/planning.py", line 314, in run
workflow.calibration()
File "/home/tobiasko/miniconda3/envs/alphadia/lib/python3.9/site-packages/alphadia/workflow/peptidecentric.py", line 476, in calibration
feature_df, fragment_df = self.extract_batch(batch_df)
File "/home/tobiasko/miniconda3/envs/alphadia/lib/python3.9/site-packages/alphadia/workflow/peptidecentric.py", line 705, in extract_batch
sns.histplot(candidates_df, x="score", hue="decoy", bins=100)
File "/home/tobiasko/miniconda3/envs/alphadia/lib/python3.9/site-packages/seaborn/distributions.py", line 1416, in histplot
p.plot_univariate_histogram(
File "/home/tobiasko/miniconda3/envs/alphadia/lib/python3.9/site-packages/seaborn/distributions.py", line 665, in plot_univariate_histogram
hist_metadata = pd.concat([
File "/home/tobiasko/.local/lib/python3.9/site-packages/pandas/core/reshape/concat.py", line 372, in concat
op = _Concatenator(
File "/home/tobiasko/.local/lib/python3.9/site-packages/pandas/core/reshape/concat.py", line 429, in __init__
raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate
0:11:41.834527 INFO: Traceback (most recent call last):
File "/home/tobiasko/miniconda3/envs/alphadia/lib/python3.9/site-packages/alphadia/cli.py", line 341, in run
plan.run()
File "/home/tobiasko/miniconda3/envs/alphadia/lib/python3.9/site-packages/alphadia/planning.py", line 358, in run
raise e
File "/home/tobiasko/miniconda3/envs/alphadia/lib/python3.9/site-packages/alphadia/planning.py", line 314, in run
workflow.calibration()
File "/home/tobiasko/miniconda3/envs/alphadia/lib/python3.9/site-packages/alphadia/workflow/peptidecentric.py", line 476, in calibration
feature_df, fragment_df = self.extract_batch(batch_df)
File "/home/tobiasko/miniconda3/envs/alphadia/lib/python3.9/site-packages/alphadia/workflow/peptidecentric.py", line 705, in extract_batch
sns.histplot(candidates_df, x="score", hue="decoy", bins=100)
File "/home/tobiasko/miniconda3/envs/alphadia/lib/python3.9/site-packages/seaborn/distributions.py", line 1416, in histplot
p.plot_univariate_histogram(
File "/home/tobiasko/miniconda3/envs/alphadia/lib/python3.9/site-packages/seaborn/distributions.py", line 665, in plot_univariate_histogram
hist_metadata = pd.concat([
File "/home/tobiasko/.local/lib/python3.9/site-packages/pandas/core/reshape/concat.py", line 372, in concat
op = _Concatenator(
File "/home/tobiasko/.local/lib/python3.9/site-packages/pandas/core/reshape/concat.py", line 429, in __init__
raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate
0:11:41.834586 ERROR: No objects to concatenate
0:11:51.922785 WARNING: WARNING: Temp mmap arrays were written to /tmp/temp_mmap_3vpm1do3. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 39,189,475,328
GeorgWa
Describe the bug
I am trying to run alphadia throughCLI using a single diaPASEF file (generated on timsTOF Flex) and the example specLib. If fails using the default parameter file. Is this expected? Are there criticial parameters that need to be changed? Or is the problem the library (generated from ASTRAL data)? The same data was searched already by DIA-NN library-fee mode without a problem.
Expected behavior exit without error
Logs see above
Version (please complete the following information):
Additional context Is it possible to use the AlphapeptDeep framework for library prediction in alphapeptdia? I still don't get why I need to provide a library at all.